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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs12720065

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr8:18400406 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.001001 (249/248818, GnomAD_exome)
G=0.003799 (477/125568, TOPMED)
G=0.001244 (150/120574, ExAC) (+ 7 more)
G=0.00296 (93/31388, GnomAD)
G=0.00431 (56/13006, GO-ESP)
G=0.00045 (5/11172, ALFA Project)
G=0.0064 (32/5008, 1000G)
G=0.003 (1/314, HapMap)
C=0.5 (2/4, SGDP_PRJ)
G=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NAT2 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 8 NC_000008.11:g.18400406C>G
GRCh37.p13 chr 8 NC_000008.10:g.18257916C>G
NAT2 RefSeqGene NG_012246.1:g.14162C>G
Gene: NAT2, N-acetyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NAT2 transcript NM_000015.3:c.403C>G L [CTA] > V [GTA] Coding Sequence Variant
arylamine N-acetyltransferase 2 NP_000006.2:p.Leu135Val L (Leu) > V (Val) Missense Variant
NAT2 transcript variant X1 XM_017012938.1:c.403C>G L [CTA] > V [GTA] Coding Sequence Variant
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Leu135Val L (Leu) > V (Val) Missense Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency (New)
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 11172 C=0.99955 G=0.00045
European Sub 8132 C=1.0000 G=0.0000
African Sub 676 C=0.993 G=0.007
African Others Sub 14 C=1.00 G=0.00
African American Sub 662 C=0.992 G=0.008
Asian Sub 60 C=1.00 G=0.00
East Asian Sub 28 C=1.00 G=0.00
Other Asian Sub 32 C=1.00 G=0.00
Latin American 1 Sub 0 C=0 G=0
Latin American 2 Sub 0 C=0 G=0
South Asian Sub 4 C=1.0 G=0.0
Other Sub 2300 C=1.0000 G=0.0000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 248818 C=0.998999 G=0.001001
gnomAD - Exomes European Sub 134296 C=0.999978 G=0.000022
gnomAD - Exomes Asian Sub 48412 C=0.99998 G=0.00002
gnomAD - Exomes American Sub 34110 C=0.99903 G=0.00097
gnomAD - Exomes African Sub 16202 C=0.98704 G=0.01296
gnomAD - Exomes Ashkenazi Jewish Sub 9774 C=1.0000 G=0.0000
gnomAD - Exomes Other Sub 6024 C=0.9997 G=0.0003
TopMed Global Study-wide 125568 C=0.996201 G=0.003799
ExAC Global Study-wide 120574 C=0.998756 G=0.001244
ExAC Europe Sub 73042 C=0.99999 G=0.00001
ExAC Asian Sub 24772 C=1.00000 G=0.00000
ExAC American Sub 11506 C=0.99896 G=0.00104
ExAC African Sub 10356 C=0.98677 G=0.01323
ExAC Other Sub 898 C=1.000 G=0.000
gnomAD - Genomes Global Study-wide 31388 C=0.99704 G=0.00296
gnomAD - Genomes European Sub 18900 C=0.99989 G=0.00011
gnomAD - Genomes African Sub 8704 C=0.9898 G=0.0102
gnomAD - Genomes East Asian Sub 1560 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 1086 C=0.9991 G=0.0009
gnomAD - Genomes American Sub 848 C=0.999 G=0.001
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99569 G=0.00431
GO Exome Sequencing Project European American Sub 8600 C=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9873 G=0.0127
ALFA Total Global 11172 C=0.99955 G=0.00045
ALFA European Sub 8132 C=1.0000 G=0.0000
ALFA Other Sub 2300 C=1.0000 G=0.0000
ALFA African Sub 676 C=0.993 G=0.007
ALFA Asian Sub 60 C=1.00 G=0.00
ALFA South Asian Sub 4 C=1.0 G=0.0
ALFA Latin American 1 Sub 0 C=0 G=0
ALFA Latin American 2 Sub 0 C=0 G=0
1000Genomes Global Study-wide 5008 C=0.9936 G=0.0064
1000Genomes African Sub 1322 C=0.9766 G=0.0234
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=0.999 G=0.001
HapMap Global Study-wide 314 C=0.997 G=0.003
HapMap African Sub 118 C=1.000 G=0.000
HapMap American Sub 106 C=0.991 G=0.009
HapMap Asian Sub 90 C=1.00 G=0.00
SGDP_PRJ Global Study-wide 4 C=0.5 G=0.5
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= G
GRCh38.p12 chr 8 NC_000008.11:g.18400406= NC_000008.11:g.18400406C>G
GRCh37.p13 chr 8 NC_000008.10:g.18257916= NC_000008.10:g.18257916C>G
NAT2 RefSeqGene NG_012246.1:g.14162= NG_012246.1:g.14162C>G
NAT2 transcript NM_000015.3:c.403= NM_000015.3:c.403C>G
NAT2 transcript NM_000015.2:c.403= NM_000015.2:c.403C>G
NAT2 transcript variant X1 XM_017012938.1:c.403= XM_017012938.1:c.403C>G
arylamine N-acetyltransferase 2 NP_000006.2:p.Leu135= NP_000006.2:p.Leu135Val
arylamine N-acetyltransferase 2 isoform X1 XP_016868427.1:p.Leu135= XP_016868427.1:p.Leu135Val
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

43 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 POLYGENYX ss20398860 Apr 05, 2004 (121)
2 PERLEGEN ss69042398 May 17, 2007 (127)
3 CGM_KYOTO ss76869171 Dec 06, 2007 (129)
4 CORNELL ss86244080 Mar 23, 2008 (129)
5 SNP500CANCER ss105440017 Feb 04, 2009 (130)
6 ILLUMINA ss120036970 Dec 01, 2009 (131)
7 ILLUMINA ss160296881 Dec 01, 2009 (131)
8 NHLBI-ESP ss342253606 May 09, 2011 (134)
9 1000GENOMES ss460256626 Sep 17, 2011 (135)
10 ILLUMINA ss480404307 Sep 08, 2015 (146)
11 1000GENOMES ss490960721 May 04, 2012 (137)
12 EXOME_CHIP ss491410758 May 04, 2012 (137)
13 TISHKOFF ss560588641 Apr 25, 2013 (138)
14 ILLUMINA ss780867823 Aug 21, 2014 (142)
15 ILLUMINA ss783552754 Aug 21, 2014 (142)
16 1000GENOMES ss1328853901 Aug 21, 2014 (142)
17 EVA_EXAC ss1689107855 Apr 01, 2015 (144)
18 ILLUMINA ss1752722184 Sep 08, 2015 (146)
19 ILLUMINA ss1917826204 Feb 12, 2016 (147)
20 ILLUMINA ss1946231108 Feb 12, 2016 (147)
21 ILLUMINA ss1959092402 Feb 12, 2016 (147)
22 HUMAN_LONGEVITY ss2301164550 Dec 20, 2016 (150)
23 TOPMED ss2470822143 Dec 20, 2016 (150)
24 GNOMAD ss2737016679 Nov 08, 2017 (151)
25 GNOMAD ss2748005933 Nov 08, 2017 (151)
26 GNOMAD ss2863932591 Nov 08, 2017 (151)
27 AFFY ss2985432612 Nov 08, 2017 (151)
28 ILLUMINA ss3022824452 Nov 08, 2017 (151)
29 CSIRBIOHTS ss3029637977 Nov 08, 2017 (151)
30 TOPMED ss3555514735 Nov 08, 2017 (151)
31 ILLUMINA ss3630009719 Oct 12, 2018 (152)
32 ILLUMINA ss3635161280 Oct 12, 2018 (152)
33 ILLUMINA ss3636898280 Oct 12, 2018 (152)
34 ILLUMINA ss3640868570 Oct 12, 2018 (152)
35 ILLUMINA ss3644964282 Oct 12, 2018 (152)
36 ILLUMINA ss3653365282 Oct 12, 2018 (152)
37 ILLUMINA ss3654194403 Oct 12, 2018 (152)
38 ILLUMINA ss3726518834 Jul 13, 2019 (153)
39 ILLUMINA ss3744577632 Jul 13, 2019 (153)
40 ILLUMINA ss3745461070 Jul 13, 2019 (153)
41 ILLUMINA ss3772953670 Jul 13, 2019 (153)
42 EVA ss3824350620 Apr 26, 2020 (154)
43 SGDP_PRJ ss3869405009 Apr 26, 2020 (154)
44 1000Genomes NC_000008.10 - 18257916 Oct 12, 2018 (152)
45 ExAC NC_000008.10 - 18257916 Oct 12, 2018 (152)
46 gnomAD - Genomes NC_000008.10 - 18257916 Jul 13, 2019 (153)
47 gnomAD - Exomes NC_000008.10 - 18257916 Jul 13, 2019 (153)
48 GO Exome Sequencing Project NC_000008.10 - 18257916 Oct 12, 2018 (152)
49 HapMap NC_000008.11 - 18400406 Apr 26, 2020 (154)
50 SGDP_PRJ NC_000008.10 - 18257916 Apr 26, 2020 (154)
51 TopMed NC_000008.11 - 18400406 Oct 12, 2018 (152)
52 dbGaP Population Frequency Project NC_000008.11 - 18400406 Apr 26, 2020 (154)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss160296881 NC_000008.9:18302195:C:G NC_000008.11:18400405:C:G (self)
40947083, 9201213, 111847170, 6184618, 808479, 21421989, ss342253606, ss460256626, ss480404307, ss490960721, ss491410758, ss560588641, ss780867823, ss783552754, ss1328853901, ss1689107855, ss1752722184, ss1917826204, ss1946231108, ss1959092402, ss2470822143, ss2737016679, ss2748005933, ss2863932591, ss2985432612, ss3022824452, ss3029637977, ss3630009719, ss3635161280, ss3636898280, ss3640868570, ss3644964282, ss3653365282, ss3654194403, ss3744577632, ss3745461070, ss3772953670, ss3824350620, ss3869405009 NC_000008.10:18257915:C:G NC_000008.11:18400405:C:G (self)
3577447, 384382868, 723004893, ss2301164550, ss3555514735, ss3726518834 NC_000008.11:18400405:C:G NC_000008.11:18400405:C:G (self)
ss20398860, ss69042398, ss76869171, ss86244080, ss105440017, ss120036970 NT_167187.1:6116061:C:G NC_000008.11:18400405:C:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs12720065

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post557+f76c771